It's because comments can have troll effects even when they're downvoted or flagged.
There's a difference between expressing a view and setting this place on fire. There's no view that can't be expressed substantively and thoughtfully if one has a mind to, but it takes work. Throwing fuel on the fire or sand in the gears is different; that's vandalism, and it destroys the free exchange of views by ruining the container—the community and site—that supports it. The container is fragile and needs protecting.
People mostly do this without realizing how destructive it is. Dealing with it requires moderators whose role is to protect the commons. That's how HN still exists as a place for (hopefully) thoughtful discussion. We'll never all agree about where to draw the line every time, but that's secondary to the point that someone needs to.
A comment crosses into trolling when it does things that are known to ruin thoughtful discussion, whether that is the intent or not. I chided the commenter upthread because they were going much further than merely (say) arguing against a rush to judgment about the OP—they were signalling bad faith with polemical swipes (e.g. 'Your prejudice that in general, "men are pigs"'). That is not thoughtful discussion, it's destructive of it.
When we ask commenters not to do this, reactions vary. Some react by taking responsibility and learn how not to produce such effects in online conversation. Many HN users have gone through that process. I had to go through it myself (it took years); I used to optimize for snark and venting too as much as the next person. If HN has anything superb about it, to use your word, it's because of the community members who do this work.
Other commenters prefer melodrama. They proclaim they're being 'censored' for their 'unpopular opinions' by mods who 'can't handle the truth', then storm out the front door with an 'enjoy your circlejerk' or two. (Typically they then walk around the building, come back in and start over with a new account.) This is the 'help help I'm being repressed' phase of the internet cycle of life. It will never go way, but I'm confident that most neutral readers notice the same signs of bad faith that mods were reacting to. How do I know that? Because otherwise our job would be impossible.
In the end the root distinction isn't about what view a commenter has on this or that topic, it's the difference between users who comment with care for the whole and those who don't. Sometimes that's because they're so agitated that they lack the self-control to do anything other than toss a hot potato into the thread. (It happens to everyone.) But often it's just that they haven't yet learned about this dynamic and why it matters. Once somebody gets that, they're motivated to participate in the community quite differently—but it isn't a question of changing their views, becoming more 'conformist' or 'groupthink' or any of that sort of thing people say. It's more akin to not littering in a city park, or to taking good care of a campsite.